eventPlot {SPLINTER} | R Documentation

## eventPlot

### Description

eventPlot

### Usage

    eventPlot(transcripts, roi_plot = NULL, bams = c(), names = c(),
      annoLabel = c("Gene A"), rspan = 1000, pfam_dom = NULL,
      showAll = TRUE)

### Arguments

`transcripts` | GRanges object
`roi_plot` | GRanges object region to plot
`bams` | character vector of bam file locations
`names` | character vector of name labels
`annoLabel` | character. annotation label
`rspan` | integer or NULL. number of basepairs to span from roi. if NULL, will consider whole gene of roi
`pfam_dom` | optional GRanges object of PFAM domains from UCSC Tables.
`showAll` | logical. TRUE = display splice junctions of entire view or FALSE = just roi.

### Value

a Gviz plot of genomic region

### Author(s)

Diana Low

### Examples

    # define BAM files
    data_path<-system.file("extdata",package="SPLINTER")
    mt<-paste(data_path,"/mt_chr14.bam",sep="")
    wt<-paste(data_path,"/wt_chr14.bam",sep="")

    # plot results
    eventPlot(transcripts=valid_tx,roi_plot=roi,bams=c(wt,mt),
     names=c('wt','mt'),rspan=1000)

[Package SPLINTER version 1.8.1 Index]